SANTA CRUZ, Calif. /PRNewswire/ — Somagenics has been awarded a second phase I SBIR grant from NIH to develop its resQ-RNATM technology for quantitative real-time PCR of fragmented RNA samples.

Fragmentation of RNA is a particular problem in tissue samples that have been preserved and stored (e.g., formaldehyde-fixed, paraffin-embedded [FFPE] specimens) or collected under sub-optimal conditions (forensic samples or biofluids containing RNases). Fragmentation greatly limits the information that can be extracted from RNA samples using current methods of analysis, including the most accurate method, real-time quantitative PCR (qPCR), as the fragments can become shorter than the minimum length required for this technology.

Somagenics’ resQ-RNATM method now allows analysis of RNA fragments as short as 23 nucleotides, whereas other methods require a minimum of ~100 nucleotides. As a result, resQ-RNATM allows RNA quantification in older FFPE samples, which represent a resource for biomarker discovery that, due to greater fragmentation, has been inaccessible until now. “resQ-RNA has great potential to help transform huge archives of biopsy specimens that currently languish in hospital collections into resources that researchers can analyze. Because these specimens are associated with patient data, that analysis can lead to discovery of biomarkers linked to disease progression and treatment response,” said Brian Johnston, CEO of Somagenics. “Such biomarkers are valuable tools for determining patient prognosis, choosing optimal treatment plans and assessing progress.”

A key feature of Somagenics’ resQ-RNATM technology involves circularization of RNA fragments followed by rolling-circle amplification, which generates concatemeric cDNA that is then PCR-amplified. The repeated sequences of the cDNA allow the use of PCR primers that each span almost the entire length of each repeat, thereby allowing analysis of sequences only slightly longer than a typical primer. The core technology of this approach has been validated and successfully employed in Somagenics’ related qPCR methods for the analysis of microRNA, miR-ID® and miR-Direct®.

Proof of principle has been established with a selection of RNAs, and this new NIH grant will fund the development of assays for an expanded repertoire of RNA targets, including transcripts relevant to breast cancer. Additionally, Somagenics will also develop custom assays for existing known targets.

Somagenics is a privately held biotech company with offices and laboratories located in Santa Cruz, California. It specializes in developing innovative technologies focused on RNA molecules as therapeutic agents and targets as well as biomarkers. Besides resQ-RNA™, the company’s RNA analysis technology platforms include miR-ID®, a novel circularization-based RT-qPCR method, miR-Direct® for microRNA analysis directly from blood samples, and the RealSeq® family of technologies for non-biased small RNA library construction for next-generation sequencing (NGS). The company’s therapeutic platform, small synthetic shRNA (sshRNA), includes development of therapeutic candidates to accelerate healing of chronic wounds in diabetic patients.

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What is RNA-Seq?

long RNAs are first converted into a library of cDNA fragments through either RNA fragmentation or DNA fragmentation. Sequencing adaptors (blue) are subsequently added to each cDNA fragment and a short sequence is obtained from each cDNA using high-throughput sequencing technology. The resulting sequence reads are aligned with the reference genome or transcriptome, and classified as three types: exonic reads, junction reads and poly(A) end-reads. These three types are used to generate a base-resolution expression profile for each gene. Nat Rev Genet 10(1):57-63 (2009)